“Paul was able to step in quickly when we required a comprehensive comparative analysis of software tools.  His analysis was thorough, well-structured and well documented, including written reports and ppt presentations.  Paul worked as a fully integrated member of the team, communicating well with management and staff and responding quickly to changes in project scope.  He handled subsequent projects with equal energy and enthusiasm, delivering his analyses quickly and with a high level of attention to detail.  Paul has significant experience and expertise in bioinformatics, particularly as it relates to mass spectrometry, and is well connected in the field.  We would strongly recommend him as an external/internal proteomics consultant on any project, large or small.”

Daniel Chelsky, Ph.D., Chief Scientific Officer, Caprion Biosciences, Inc.


“It is a pleasure working with Spectragen.  Our mass informatics needs are somewhat complex, and require the development of tools for processes that are highly exploratory.  I know when talking with Paul that we can work through issues that range from scientific process to mass spectrometer function to algorithms for data analysis and software interface.  The broad knowledge-base of Spectragen makes a big difference for us.”

Cambridge, MA Mass Spec Service Provider




A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline.

J Proteome Res. 2016 Mar 4;15(3):1023-32. doi: 10.1021/acs.jproteome.5b01091. Epub 2016 Feb 25.

Rudnick PA(1), Markey SP(2), Roth J(2), Mirokhin Y(2), Yan X(2), Tchekhovsko DV(2), Edwards NJ(3), Thangudu RR(4), Ketchum KA(4), Kinsinger CR(5), Mesri M(5), Rodriguez H(5), Stein SE(2)

(1)Spectragen Informatics, Bainbridge Island, Washington 98110, United States. (2)Biomolecular Measurement Division, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States. (3)Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, D.C. 20007, United States. (4)ESAC, Inc., Rockville, Maryland 20850, United States. (5)Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States.

Tandem mass spectral libraries of peptides in digests of individual proteins: Human Serum Albumin (HSA).

Mol Cell Proteomics. 2014 Sep;13(9):2435-49. doi: 10.1074/mcp.O113.037135. Epub 2014 Jun 2.

Dong Q(1), Yan X(1), Kilpatrick LE(1), Liang Y(1), Mirokhin YA(1), Roth JS(1), Rudnick PA(1), Stein SE(1).

(1)From the Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States.

Improved normalization of systematic biases affecting ion current measurements in label-free proteomics data.

Mol Cell Proteomics. 2014 May;13(5):1341-51. doi: 10.1074/mcp.M113.030593. Epub 2014 Feb 21.

Rudnick PA(1), Wang X, Yan X, Sedransk N, Stein SE.

(1)Mass Spectrometry Data Center, National Institute of Standards and Technology, Gaithersburg, Maryland;

Metabolite profiling of a NIST Standard Reference Material for human plasma (SRM1950): GC-MS, LC-MS, NMR, and clinical laboratory analyses, libraries, and web-based resources.

Anal Chem. 2013 Dec 17;85(24):11725-31. doi: 10.1021/ac402503m. Epub 2013 Dec 3.

Simón-Manso Y(1), Lowenthal MS, Kilpatrick LE, Sampson ML, Telu KH, Rudnick PA, Mallard WG, Bearden DW, Schock TB, Tchekhovskoi DV, Blonder N, Yan X, Liang Y, Zheng Y, Wallace WE, Neta P, Phinney KW, Remaley AT, Stein SE.

(1)Biomolecular Measurement Division, National Institute of Standards and Technology , Gaithersburg, Maryland 20899-8380, United States.

Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics.

J Proteome Res. 2013 Dec 6;12(12):5666-80. doi: 10.1021/pr400611h. Epub 2013 Nov 14.

Walmsley SJ(1), Rudnick PA, Liang Y, Dong Q, Stein SE, Nesvizhskii AI.

(1)Department of Pathology, University of Michigan , 4237 Medical Science I, 1301 Catherine Road, Ann Arbor, Michigan 48109, United States.

Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.

Mol Cell Proteomics. 2010 Feb;9(2):225-41. doi: 10.1074/mcp.M900223-MCP200. Epub 2009 Oct 16.

Rudnick PA(1), Clauser KR, Kilpatrick LE, Tchekhovskoi DV, Neta P, Blonder N, Billheimer DD, Blackman RK, Bunk DM, Cardasis HL, Ham AJ, Jaffe JD, Kinsinger CR, Mesri M, Neubert TA, Schilling B, Tabb DL, Tegeler TJ, Vega-Montoto L, Variyath, AM, Wang M, Wang P, Whiteaker JR, Zimmerman LJ, Carr SA, Fisher SJ, Gibson BW, Paulovich AG, Regnier FE, Rodriguez H, Spiegelman C, Tempst P, Liebler DC, Stein SE.

(1)National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma.

Nat Biotechnol. 2009 Jul;27(7):633-41. doi: 10.1038/nbt.1546. Epub 2009 Jun 28.

Addona TA(1), Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander A, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA.

Full listing on Pubmed and Google Scholar